Natural GMOs Part 31. Bacteria mate with worms among the roots and leaves.

First, the Pundit's take home message

• In the gut, in the soil, and on plants and around their roots, movement of genes between species is completely natural .

New Evidence Suggests Genes in Parasites Were Acquired From Bacteria

NC State U Press release May 20, 2003

Genetic scientists studying a group of disease-causing parasites have identified 12 genes that appear to have been acquired from bacteria. Some of the genes enable the parasites, called nematodes, to attack and damage their hosts, said Dr. David Bird, study director and associate director of the Center for the Biology of Nematode Parasitism at North Carolina State University.

The study is the first to compare fully sequenced genomes to identify genes that have migrated “horizontally” from one species to another, in this case from soil bacteria to root-knot nematodes that infest plants. Identifying and targeting the genes responsible for parasitism may one day yield effective measures to combat these costly and disabling diseases.

The study, described in a paper published on May 19 [2003] in Genome Biology, is funded by a $2.6 million grant from the National Science Foundation and was performed in collaboration with scientists at NC State’s Bioinformatics Research Center and at Washington University.

Nematodes are the largest and most destructive group of animals in the world. Billions of people, companion animals, and livestock suffer debilitating diseases caused by hookworm, roundworm, heartworm, and other nematodes. Plant-parasitic nematodes cause an estimated $100 billion a year in crop damage worldwide.

The findings also have significant implications for understanding the evolution of species, in which gene transfer from one species to another appears to play an important role.

Bird and his colleagues examined the genomes of three species of the root-knot nematode Meloidogyne, which deforms the roots of many crops including tobacco and tomato. The nematodes “hijack the plant’s developmental pathways and form a feeding site in the roots, inhibiting the plant’s growth,” said Bird.

“What makes the parasitic nematodes different from the free-living nematodes that do not harm plants and animals? This is the question scientists want to answer,” said Bird. “The differences must be explained by their genes.”

Bird and his colleagues developed two “phylogenetic filters,” or computer methods of comparing genetic codes of different species. One filter found genes in the root-knot nematodes that were present in bacteria but were not present in the model non-parasitic nematode C. elegans or in fruit flies, which share an evolutionary ancestor with nematodes. The genes that passed through the first phylogenetic filter were then compared to a comprehensive genetic database of proteins to eliminate any other animal genes.

The 12 genes that passed through both phylogenetic filters had best matches to bacterial genes and were identified as candidates for horizontal gene transfer from bacteria. “This is a surprisingly large number of genes,” said Bird.

Six of the 12 genes had been suggested by other researchers as possibly originating from bacteria, based on analysis of single genes or other evidence, and six were newly identified based solely on the genomic comparisons performed by Bird’s group.

Seven of the candidate genes of bacterial origin are associated with enzymes that degrade cell walls or deform cell structure. “We started with no preconceived notions of the biological role of any transferred genes, so to have found mainly genes that have an apparent role in parasitism – that was a real surprise,” said Elizabeth H. Scholl, an NC State doctoral student who helped design and implement the genomic comparisons.

Four of the candidate genes in the root-knot nematodes most closely matched genes in a group of nitrogen-fixing soil bacteria called rhizobia, which also live in and deform the roots of plants, but with beneficial rather than harmful effects. One match was to the rhizobial NodL gene, which is associated with formation of root nodules and was previously thought only to reside in rhizobia. These genes appear to have been transferred from the soil bacteria to presumably once-harmless nematodes, creating new species of parasites.

Bird hypothesizes that the acquisition of genes from bacteria was a key event in the evolution of nematode species. The first step was probably a symbiotic, or physically close and mutually beneficial, relationship between nematodes and bacteria, as is the case between certain bacteria living in nematodes that cause human diseases, such as elephantiasis and river blindness.

Bird is designing further experiments to verify horizontal gene transfer in nematodes and to identify which genes may be promising targets for developing disease-control methods.

Press release NC State University
Media Contacts:
Dr. David Bird, 919/515-6813
Mick Kulikowski, News Services, 919/515-3470

The abstract of the Genome Biology paper follows.

“Horizontally transferred genes in plant-parasitic nematodes: A high-throughput genomic approach”

Authors: Elizabeth H. Scholl, Jeffrey Thorne, David McK. Bird, North Carolina State University; James McCarter, Washington University and Divergence, Inc.
Date: Published in the May 19 2003 edition of Genome Biology

Abstract: Published accounts of horizontally acquired genes in plant-parasitic nematodes have not been the result of a specific search for gene transfer per se, but rather have emerged from characterization of individual genes. We present a method for a high-throughput genome screen for horizontally acquired genes, illustrated using expressed sequence tag (EST) data from three species of root-knot nematode, Meloidogyne spp. Our approach identified the previously postulated horizontally transferred genes and revealed six new candidates. Screening was partially dependent upon sequence quality, with more candidates identified from clustered sequences than from raw EST data. Computational and experimental methods verified the horizontal gene transfer candidates as bona fide nematode genes. Phylogenetic analysis implicated rhizobial ancestors as donors of horizontally acquired genes in Meloidogyne. High-throughput genomic screening is an effective way to identify horizontal gene transfer candidates. Transferred genes that have undergone amelioration of nucleotide composition and codon bias have been identified using this approach. Analysis of these horizontally transferred gene candidates suggests a link between horizontally transferred genes in Meloidogyne and parasitism.

Horizontal gene transfer from bacteria and fungi as a driving force in the evolution of plant parasitism in nematodes
John T Jones, Cleber Furlanetto and Taisei Kikuchi
Published online: 01 July 2005

Phylogenetic studies have shown that parasitism of plants by nematodes has arisen independently on at least three separate occasions. We argue that horizontal gene transfer has played a critical role in the evolution of plant parasitism on each occasion. In addition, we discuss evidence that suggests this process has driven the evolution of other life strategies within the Nematoda and that it may be considerably more common within the Phylum than commonly thought. We review recent literature that shows horizontal gene transfer to nematodes has occurred from both bacteria and fungi. GENETICS - PARASITISM - PLANT-PARASITIC NEMATODES

Journal Nematology
Publisher Brill Academic Publishers
ISSN 1388-5545 (Print) 1568-5411 (Online)
Issue Volume 7, Number 5 / July, 2005
DOI 10.1163/156854105775142919
Pages 641-646

A Functional Screen Identifies Lateral Transfer of ß-Glucuronidase (gus) from Bacteria to Fungi

Lateral gene transfer (LGT) from prokaryotes to microbial eukaryotes is usually detected by chance through genome-sequencing projects. Here, we explore a different, hypothesis-driven approach. We show that the fitness advantage associated with the transferred gene, typically invoked only in retrospect, can be used to design a functional screen capable of identifying postulated LGT cases. We hypothesized that ß-glucuronidase (gus) genes may be prone to LGT from bacteria to fungi (thought to lack gus) because this would enable fungi to utilize glucuronides in vertebrate urine as a carbon source. Using an enrichment procedure based on a glucose-releasing glucuronide analog (cellobiouronic acid), we isolated two gus+ ascomycete fungi from soils (Penicillium canescens and Scopulariopsis sp.). A phylogenetic analysis suggested that their gus genes, as well as the gus genes identified in genomic sequences of the ascomycetes Aspergillus nidulans and Gibberella zeae, had been introgressed laterally from high-GC gram+ bacteria. Two such bacteria (Arthrobacter spp.), isolated together with the gus+ fungi, appeared to be the descendants of a bacterial donor organism from which gus had been transferred to fungi. This scenario was independently supported by similar substrate affinities of the encoded ß-glucuronidases, the absence of introns from fungal gus genes, and the similarity between the signal peptide-encoding 5' extensions of some fungal gus genes and the Arthrobacter sequences upstream of gus. Differences in the sequences of the fungal 5' extensions suggested at least two separate introgression events after the divergence of the two main Euascomycete classes. We suggest that deposition of glucuronides on soils as a result of the colonization of land by vertebrates may have favored LGT of gus from bacteria to fungi in soils.

Key Words: Lateral gene transfer • gus • ß-glucuronidase • bacteria • fungi

Molecular Biology and Evolution vol. 22 no. 2 © Society for Molecular Biology and Evolution 2005; all rights reserved.
Peter Wenzl, Laurie Wong1, Kim Kwang-won2 and Richard A. Jefferson
Center for the Application of Molecular Biology to International Agriculture (CAMBIA), Canberra, Australia
E-mail peter--AT--cambia.org.

Horizontal Gene Transfer of Glycosyl Hydrolases of the Rumen Fungi
S. Garcia-Vallve´, A. Romeu, and J. Palau

Department of Biochemistry and Biotechnology, Rovira i Virgili University, Catalonia, Spain

By combining analyses of G1C content and patterns of codon usage and constructing phylogenetic trees, we describe the gene transfer of an endoglucanase (celA) from the rumen bacteria Fibrobacter succinogenes to the rumen fungi Orpinomyces joyonii. The strong similarity between different glycosyl hydrolases of rumen fungi and bacteria suggests that most, if not all, of the glycosyl hydrolases of rumen fungi that play an important role in the degradation of cellulose and other plant polysaccharides were acquired by horizontal gene transfer events. This acquisition allows fungi to establish a habitat within a new environmental niche: the rumen of the herbivorous mammals for which cellulose and plant hemicellulose constitute the main raw nutritive substrate.

Microbiology 151 (2005), 121-133; DOI 10.1099/mic.0.27353-0
© 2005 Society for General Microbiology